From 1 July 1998 a new financial regulatory framework came into effect, in response to the recommendations of the Financial System Inquiry (the Wallis Committee). Under the new structure a single prudential supervisor, the Australian Prudential Regulation Authority (APRA), was established to take responsibility for the supervision of banks, life and general insurance companies and superannuation funds. The Australian Securities and Investments Commission (ASIC) assumed responsibility for market integrity and consumer protection across the financial system. The Reserve Bank retained responsibility for monetary policy and the maintenance of financial stability, including stability of the payments system.

From 1 July 1999 building societies and credit unions have been supervised by APRA. APRA supervises benefit funds of friendly societies under the Life Insurance Act 1995 (Cwlth), while health benefit funds of friendly societies are regulated by the Private Health Insurance Administration Council under the National Health Act 1959(Cwlth). Prior to 1 July 1999, building societies, credit unions and friendly societies were regulated under state legislation.

On 1 July 2000 regulation of self-managed superannuation funds was transferred to the Australian Taxation Office (ATO).From September 2001 the Financial Sector (Collection of Statistics) Act 2001 (Cwlth) provided APRA with powers to collect information previously collected under the range of legislation for which it was responsible, and under the Financial Corporations Act administered by the Reserve Bank. The new legislation enables harmonised and consistent data collection from financial institutions. APRA commenced data collection from registered financial corporations from March 2003.